******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.10.0 (Release date: Wed May 21 10:35:36 2014 +1000) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme.nbcr.net. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** DATAFILE= motifs/363/363.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 43243 1.0000 500 1813 1.0000 500 36808 1.0000 500 13333 1.0000 500 4956 1.0000 500 14477 1.0000 500 47952 1.0000 500 38369 1.0000 500 14696 1.0000 500 48153 1.0000 500 38581 1.0000 500 15126 1.0000 500 49521 1.0000 500 44224 1.0000 500 50551 1.0000 500 50586 1.0000 500 44759 1.0000 500 7755 1.0000 500 45022 1.0000 500 45831 1.0000 500 12588 1.0000 500 52418 1.0000 500 33611 1.0000 500 37218 1.0000 500 46409 1.0000 500 50015 1.0000 500 49605 1.0000 500 50151 1.0000 500 48711 1.0000 500 46300 1.0000 500 49811 1.0000 500 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme motifs/363/363.seqs.fa -oc motifs/363 -dna -minw 12 -maxw 21 -nmotifs 3 -maxsize 500000 model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 12 maxw= 21 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 31 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 15500 N= 31 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.262 C 0.251 G 0.221 T 0.266 Background letter frequencies (from dataset with add-one prior applied): A 0.262 C 0.251 G 0.221 T 0.266 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 28 llr = 245 E-value = 8.1e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :6822868a327 pos.-specific C a1345:4::7:2 probability G :1::31:2::81 matrix T :1:4:1:::::: bits 2.2 2.0 * 1.7 * * 1.5 * * Relative 1.3 * ** * Entropy 1.1 * * ****** (12.6 bits) 0.9 * * ****** 0.7 * * ******** 0.4 * ********** 0.2 ************ 0.0 ------------ Multilevel CAATCAAAACGA consensus CCG CG AA sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 1813 476 1.53e-07 CTCTCGAAAC CAACCAAAACGA TCGAGCTGCC 50015 123 1.52e-06 AGAACGTAAC CAACAAAAACGA GATTGGAAAC 15126 458 4.37e-06 TCGCTTCTGA CAAACAAGACGA GTTTGCACAG 38369 251 4.37e-06 AGCTTTGGGC CTATGAAAACGA CCCAATCTAA 36808 22 4.37e-06 AAAGAAACTG CAACCACGACGA CGATGACACA 45022 322 8.18e-06 TGTTTCCGGA CAATCGAAACGA TCGTATCCAC 37218 277 9.68e-06 GCTTCCGTCC CACACACAACGA ATCACAGCCC 52418 300 9.68e-06 ACTTCCGTCC CACACACAACGA ATCACAGCCC 7755 145 9.68e-06 AAGAACGAAC CAAAGAAAACGG CTTTTTGGAG 49605 478 1.12e-05 CATCGACAAT CGATCAAAACGC AGCAAATTAC 48153 364 1.25e-05 ACATTATCGT CGACCAAAACGC CATCTAAATC 49811 48 1.65e-05 CATGTCGATA CAACGAAAAAGG CGGAGATGAT 45831 155 1.65e-05 TTCAAGCCCG CCATGAAAAAGA ATATTGTAAA 13333 325 1.65e-05 TTAATGCTGG CCATGAAAAAGA ATCGCTATTT 46409 5 2.09e-05 TCAA CAACATAAACGA GGTTTCTGTT 38581 294 2.87e-05 ACTCACGACC CAATCACGACAA CACGGGAGCC 50151 184 4.74e-05 AAGCCTGCCA CTAAGAAAACGC GCTTCCTATT 44224 46 4.74e-05 CCATACACTT CACCCAAAAAAA CCAATTTACG 43243 409 5.74e-05 CTCCCGAGTA CACCAACAAAGA GCGCGTGGAG 46300 183 7.49e-05 CTACGAAAGT CAATCTAGACGG AAATAAGAAA 4956 175 9.51e-05 TAGAGGCCAT CGATAACAACAA CTCAATCACT 47952 403 1.19e-04 CAAAATATTA CTATCACAACAC ATTCCAACTG 50586 59 1.47e-04 TCCATAGTTG CACAGACAAAGG AAAGTAGCGA 14696 318 1.47e-04 TTGTGGAATT CACCCTCAACAA TCTTGATGGA 12588 434 1.67e-04 TCGGTACAAA CCCTGGAAACGA CCCGGCTACC 48711 356 2.26e-04 GACGAGGTCA CTATGTAAAAGC GTGACACCTA 50551 342 2.52e-04 CTCTCATATT CCATCAAGCCGA AGGGATTGGA 44759 363 3.70e-04 CAGGACTACG CGACAACGAAAA TACCATAGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1813 1.5e-07 475_[+1]_13 50015 1.5e-06 122_[+1]_366 15126 4.4e-06 457_[+1]_31 38369 4.4e-06 250_[+1]_238 36808 4.4e-06 21_[+1]_467 45022 8.2e-06 321_[+1]_167 37218 9.7e-06 276_[+1]_212 52418 9.7e-06 299_[+1]_189 7755 9.7e-06 144_[+1]_344 49605 1.1e-05 477_[+1]_11 48153 1.3e-05 363_[+1]_125 49811 1.6e-05 47_[+1]_441 45831 1.6e-05 154_[+1]_334 13333 1.6e-05 324_[+1]_164 46409 2.1e-05 4_[+1]_484 38581 2.9e-05 293_[+1]_195 50151 4.7e-05 183_[+1]_305 44224 4.7e-05 45_[+1]_443 43243 5.7e-05 408_[+1]_80 46300 7.5e-05 182_[+1]_306 4956 9.5e-05 174_[+1]_314 47952 0.00012 402_[+1]_86 50586 0.00015 58_[+1]_430 14696 0.00015 317_[+1]_171 12588 0.00017 433_[+1]_55 48711 0.00023 355_[+1]_133 50551 0.00025 341_[+1]_147 44759 0.00037 362_[+1]_126 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=28 1813 ( 476) CAACCAAAACGA 1 50015 ( 123) CAACAAAAACGA 1 15126 ( 458) CAAACAAGACGA 1 38369 ( 251) CTATGAAAACGA 1 36808 ( 22) CAACCACGACGA 1 45022 ( 322) CAATCGAAACGA 1 37218 ( 277) CACACACAACGA 1 52418 ( 300) CACACACAACGA 1 7755 ( 145) CAAAGAAAACGG 1 49605 ( 478) CGATCAAAACGC 1 48153 ( 364) CGACCAAAACGC 1 49811 ( 48) CAACGAAAAAGG 1 45831 ( 155) CCATGAAAAAGA 1 13333 ( 325) CCATGAAAAAGA 1 46409 ( 5) CAACATAAACGA 1 38581 ( 294) CAATCACGACAA 1 50151 ( 184) CTAAGAAAACGC 1 44224 ( 46) CACCCAAAAAAA 1 43243 ( 409) CACCAACAAAGA 1 46300 ( 183) CAATCTAGACGG 1 4956 ( 175) CGATAACAACAA 1 47952 ( 403) CTATCACAACAC 1 50586 ( 59) CACAGACAAAGG 1 14696 ( 318) CACCCTCAACAA 1 12588 ( 434) CCCTGGAAACGA 1 48711 ( 356) CTATGTAAAAGC 1 50551 ( 342) CCATCAAGCCGA 1 44759 ( 363) CGACAACGAAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 15159 bayes= 9.6845 E= 8.1e-003 -1145 199 -1145 -1145 112 -81 -63 -89 152 -1 -1145 -1145 -29 51 -1145 69 -55 99 54 -1145 158 -1145 -163 -89 129 51 -1145 -1145 158 -1145 -4 -1145 188 -281 -1145 -1145 12 151 -1145 -1145 -29 -1145 183 -1145 137 -49 -63 -1145 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 28 E= 8.1e-003 0.000000 1.000000 0.000000 0.000000 0.571429 0.142857 0.142857 0.142857 0.750000 0.250000 0.000000 0.000000 0.214286 0.357143 0.000000 0.428571 0.178571 0.500000 0.321429 0.000000 0.785714 0.000000 0.071429 0.142857 0.642857 0.357143 0.000000 0.000000 0.785714 0.000000 0.214286 0.000000 0.964286 0.035714 0.000000 0.000000 0.285714 0.714286 0.000000 0.000000 0.214286 0.000000 0.785714 0.000000 0.678571 0.178571 0.142857 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CA[AC][TCA][CG]A[AC][AG]A[CA][GA]A -------------------------------------------------------------------------------- Time 7.20 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 5 llr = 104 E-value = 1.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A a::82a6::::::6::a:aa: pos.-specific C :2426::8::a282a4::::6 probability G :86:2:::62:::::6:a::4 matrix T ::::::4248:822::::::: bits 2.2 * 2.0 * * * * **** 1.7 * * * * **** 1.5 ** * * * **** Relative 1.3 ** * * * **** * **** Entropy 1.1 **** * ****** ******* (30.1 bits) 0.9 **** ******** ******* 0.7 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel AGGACAACGTCTCACGAGAAC consensus CCCA TTTG CTC C G sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 37218 223 2.14e-12 ACTCCTGGTA AGGACAACGTCTCACCAGAAG TTCAATTGCC 52418 240 2.14e-12 ACTCCCGGTA AGGACAACGTCTCACCAGAAG TTCAATCACT 45022 458 5.65e-10 GTCTTCGAGA AGCAGAATTTCTCCCGAGAAC AAACCCGGCA 50551 200 7.25e-10 TTCCAATAGG AGGAAATCTTCCTACGAGAAC CCTGCTCTAT 14696 129 1.63e-09 TTTCTAGTCC ACCCCATCGGCTCTCGAGAAC CGCCTCTTCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37218 2.1e-12 222_[+2]_257 52418 2.1e-12 239_[+2]_240 45022 5.7e-10 457_[+2]_22 50551 7.3e-10 199_[+2]_280 14696 1.6e-09 128_[+2]_351 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=5 37218 ( 223) AGGACAACGTCTCACCAGAAG 1 52418 ( 240) AGGACAACGTCTCACCAGAAG 1 45022 ( 458) AGCAGAATTTCTCCCGAGAAC 1 50551 ( 200) AGGAAATCTTCCTACGAGAAC 1 14696 ( 129) ACCCCATCGGCTCTCGAGAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14880 bayes= 12.4823 E= 1.0e+002 193 -897 -897 -897 -897 -33 185 -897 -897 67 144 -897 161 -33 -897 -897 -39 125 -14 -897 193 -897 -897 -897 119 -897 -897 59 -897 167 -897 -41 -897 -897 144 59 -897 -897 -14 159 -897 199 -897 -897 -897 -33 -897 159 -897 167 -897 -41 119 -33 -897 -41 -897 199 -897 -897 -897 67 144 -897 193 -897 -897 -897 -897 -897 218 -897 193 -897 -897 -897 193 -897 -897 -897 -897 125 85 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 1.0e+002 1.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.400000 0.600000 0.000000 0.800000 0.200000 0.000000 0.000000 0.200000 0.600000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.400000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.600000 0.400000 0.000000 0.000000 0.200000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.800000 0.000000 0.200000 0.600000 0.200000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.600000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.400000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- A[GC][GC][AC][CAG]A[AT][CT][GT][TG]C[TC][CT][ACT]C[GC]AGAA[CG] -------------------------------------------------------------------------------- Time 14.68 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 31 llr = 249 E-value = 1.2e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::::11::::5 pos.-specific C 1:1554:4:67: probability G ::413:::5:15 matrix T 9a543595542: bits 2.2 2.0 1.7 * 1.5 ** * Relative 1.3 ** * Entropy 1.1 ** * ** * (11.6 bits) 0.9 ** * **** 0.7 **** ******* 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TTTCCTTTGCCA consensus GTGC CTT G sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 36808 478 9.33e-07 TTTGTGATAC TTGTCTTTGCCA TCGTCATCAA 14477 426 1.51e-06 AGCTCCAGCA TTGCCTTTTCCA ATCATGCAGA 38581 469 2.28e-06 AATACAAAAA TTTCCCTTGCCA TTTTTGCTGG 49521 339 6.73e-06 CTCGCAGCCT TTGCGCTTTCCG GCAGGCGGCG 50015 374 1.05e-05 ACCATAAAAA TTTCGTTCGCCA TCGGAGTAAT 46409 133 1.05e-05 ATACACGCCG TTTTCCTCTCCA GTCGCTATTG 48711 487 2.39e-05 ATTTTGCCAG TTTCTCTTGTCG CG 14696 77 2.65e-05 TCGCGACGCT TTGCCATTGCCG TGGGAGTCTT 37218 387 3.32e-05 CATCGTCGTT TTGTGTTCTTCA ATAGAACTAC 52418 411 3.32e-05 CATCGTCGTT TTGTGTTCTTCA ATAGAACTAC 46300 211 4.57e-05 GAAACCTCAA TTTCCATTTCCA GCATAATTAT 50586 174 5.58e-05 ACCAACTTGG TTGCCCTTGTTG GTCGTTCGCA 44759 50 6.89e-05 AGAATACTGG TTTTTCTTGCTG AGTCTATGTG 7755 88 7.65e-05 CTACGTTTGG TTCCGTTTTTCG TTCTTTGCAC 48153 336 7.65e-05 CGTATCCGCG TTCCTCTCTCCG ACCAACACAT 44224 243 8.47e-05 GCTAGATTCC TTTTTTTCGCGG TCTACCGAGA 1813 75 8.47e-05 GTTCACAATG TTTGTTTTTTCG TTTCCCAACA 50151 485 9.28e-05 CCGCTTCCAC TTGCCTTAGCCG CAGA 45022 294 9.28e-05 CAAACATTAT TTTTCCATGCCA GTCTTTTGTT 38369 376 9.28e-05 CATCCGAATG TTTGGTTCTTCG CGGAAATCGG 13333 229 9.28e-05 AGGAAACGTT TTGTTCTTTCTA TTCGGCAAAC 12588 304 1.02e-04 GCGGGGGGCT TTGCCCACGCCA TGGAAGACCT 50551 76 1.30e-04 TTGGTCCTCG TTTGCTTCTCTG GAAGAACTTC 4956 254 1.30e-04 TACTGAGAAT TTCCTCTTTTCA ACCTGGGGGA 49605 349 1.64e-04 AGGGTCATTA TTTGCTTCTCGA TGAAGGTGAA 15126 31 1.64e-04 ATAGAAACGT TTGTTTACTCCG ATGCGGTAAT 47952 479 1.77e-04 GCTGTGGCAT TTGTCATTGCGA ATCAGACAAA 43243 487 3.14e-04 ATCAACCACA TCTTCCTTGTCG TC 33611 18 4.19e-04 GCGGTTGCGC CTGTCTTTGTTG TGACGTTGGC 45831 436 4.19e-04 GATTCCACTT CTCCGTTCGCCA CTGTGTGGCA 49811 266 6.66e-04 GCTTCAAAGG TTTTGTTGGTGA GCCTAATGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36808 9.3e-07 477_[+3]_11 14477 1.5e-06 425_[+3]_63 38581 2.3e-06 468_[+3]_20 49521 6.7e-06 338_[+3]_150 50015 1.1e-05 373_[+3]_115 46409 1.1e-05 132_[+3]_356 48711 2.4e-05 486_[+3]_2 14696 2.6e-05 76_[+3]_412 37218 3.3e-05 386_[+3]_102 52418 3.3e-05 410_[+3]_78 46300 4.6e-05 210_[+3]_278 50586 5.6e-05 173_[+3]_315 44759 6.9e-05 49_[+3]_439 7755 7.6e-05 87_[+3]_401 48153 7.6e-05 335_[+3]_153 44224 8.5e-05 242_[+3]_246 1813 8.5e-05 74_[+3]_414 50151 9.3e-05 484_[+3]_4 45022 9.3e-05 293_[+3]_195 38369 9.3e-05 375_[+3]_113 13333 9.3e-05 228_[+3]_260 12588 0.0001 303_[+3]_185 50551 0.00013 75_[+3]_413 4956 0.00013 253_[+3]_235 49605 0.00016 348_[+3]_140 15126 0.00016 30_[+3]_458 47952 0.00018 478_[+3]_10 43243 0.00031 486_[+3]_2 33611 0.00042 17_[+3]_471 45831 0.00042 435_[+3]_53 49811 0.00067 265_[+3]_223 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=31 36808 ( 478) TTGTCTTTGCCA 1 14477 ( 426) TTGCCTTTTCCA 1 38581 ( 469) TTTCCCTTGCCA 1 49521 ( 339) TTGCGCTTTCCG 1 50015 ( 374) TTTCGTTCGCCA 1 46409 ( 133) TTTTCCTCTCCA 1 48711 ( 487) TTTCTCTTGTCG 1 14696 ( 77) TTGCCATTGCCG 1 37218 ( 387) TTGTGTTCTTCA 1 52418 ( 411) TTGTGTTCTTCA 1 46300 ( 211) TTTCCATTTCCA 1 50586 ( 174) TTGCCCTTGTTG 1 44759 ( 50) TTTTTCTTGCTG 1 7755 ( 88) TTCCGTTTTTCG 1 48153 ( 336) TTCCTCTCTCCG 1 44224 ( 243) TTTTTTTCGCGG 1 1813 ( 75) TTTGTTTTTTCG 1 50151 ( 485) TTGCCTTAGCCG 1 45022 ( 294) TTTTCCATGCCA 1 38369 ( 376) TTTGGTTCTTCG 1 13333 ( 229) TTGTTCTTTCTA 1 12588 ( 304) TTGCCCACGCCA 1 50551 ( 76) TTTGCTTCTCTG 1 4956 ( 254) TTCCTCTTTTCA 1 49605 ( 349) TTTGCTTCTCGA 1 15126 ( 31) TTGTTTACTCCG 1 47952 ( 479) TTGTCATTGCGA 1 43243 ( 487) TCTTCCTTGTCG 1 33611 ( 18) CTGTCTTTGTTG 1 45831 ( 436) CTCCGTTCGCCA 1 49811 ( 266) TTTTGTTGGTGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 15159 bayes= 8.93074 E= 1.2e+002 -1160 -196 -1160 182 -1160 -296 -1160 186 -1160 -96 92 77 -1160 85 -78 66 -1160 95 22 -4 -144 62 -1160 96 -144 -1160 -1160 177 -302 62 -277 105 -1160 -1160 122 86 -1160 136 -1160 42 -1160 150 -78 -72 98 -1160 113 -1160 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 31 E= 1.2e+002 0.000000 0.064516 0.000000 0.935484 0.000000 0.032258 0.000000 0.967742 0.000000 0.129032 0.419355 0.451613 0.000000 0.451613 0.129032 0.419355 0.000000 0.483871 0.258065 0.258065 0.096774 0.387097 0.000000 0.516129 0.096774 0.000000 0.000000 0.903226 0.032258 0.387097 0.032258 0.548387 0.000000 0.000000 0.516129 0.483871 0.000000 0.645161 0.000000 0.354839 0.000000 0.709677 0.129032 0.161290 0.516129 0.000000 0.483871 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TT[TG][CT][CGT][TC]T[TC][GT][CT]C[AG] -------------------------------------------------------------------------------- Time 21.92 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 43243 3.52e-04 388_[+2(2.04e-06)]_91 1813 2.32e-04 74_[+3(8.47e-05)]_389_\ [+1(1.53e-07)]_13 36808 8.22e-05 21_[+1(4.37e-06)]_444_\ [+3(9.33e-07)]_11 13333 9.51e-03 228_[+3(9.28e-05)]_84_\ [+1(1.65e-05)]_164 4956 1.53e-02 174_[+1(9.51e-05)]_314 14477 1.18e-02 425_[+3(1.51e-06)]_63 47952 4.61e-02 500 38369 1.02e-03 250_[+1(4.37e-06)]_113_\ [+3(9.28e-05)]_113 14696 1.70e-07 76_[+3(2.65e-05)]_40_[+2(1.63e-09)]_\ 351 48153 7.32e-03 335_[+3(7.65e-05)]_16_\ [+1(1.25e-05)]_125 38581 3.24e-04 293_[+1(2.87e-05)]_163_\ [+3(2.28e-06)]_20 15126 6.11e-03 457_[+1(4.37e-06)]_31 49521 4.76e-03 338_[+3(6.73e-06)]_150 44224 8.47e-03 45_[+1(4.74e-05)]_185_\ [+3(8.47e-05)]_246 50551 5.41e-07 199_[+2(7.25e-10)]_280 50586 1.55e-02 173_[+3(5.58e-05)]_315 44759 4.34e-02 49_[+3(6.89e-05)]_439 7755 6.19e-03 87_[+3(7.65e-05)]_45_[+1(9.68e-06)]_\ 344 45022 1.48e-08 293_[+3(9.28e-05)]_16_\ [+1(8.18e-06)]_124_[+2(5.65e-10)]_22 45831 1.32e-02 154_[+1(1.65e-05)]_334 12588 7.97e-03 87_[+2(9.41e-05)]_392 52418 3.80e-11 239_[+2(2.14e-12)]_39_\ [+1(9.68e-06)]_99_[+3(3.32e-05)]_78 33611 3.61e-01 500 37218 3.80e-11 222_[+2(2.14e-12)]_33_\ [+1(9.68e-06)]_98_[+3(3.32e-05)]_102 46409 1.42e-03 4_[+1(2.09e-05)]_116_[+3(1.05e-05)]_\ 356 50015 1.27e-04 122_[+1(1.52e-06)]_239_\ [+3(1.05e-05)]_115 49605 1.14e-02 477_[+1(1.12e-05)]_11 50151 2.36e-02 183_[+1(4.74e-05)]_289_\ [+3(9.28e-05)]_4 48711 3.66e-02 486_[+3(2.39e-05)]_2 46300 7.19e-03 182_[+1(7.49e-05)]_16_\ [+3(4.57e-05)]_278 49811 3.45e-02 47_[+1(1.65e-05)]_441 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************